[gmx-users] Gromacs-4.0.2: energy minimization error in parallel version

[Berk Hess]

Hi,

I fixed the bug for version 4.0.3.
There was also a bug with writing the forces at the end
with nstfout=0.

But if you are minimizing for starting a md simulation,
you do not need cg, steepest descents is enough
(with em_tol of 1000 or 100).

Note that in 4.0 you can now minimize with constraints,
box for water and other molecules.

If you really need to run parallel cg now, you can use
the -pd switch of mdrun.

Berk



> Date: Sat, 22 Nov 2008 00:37:18 +0530
> From: suman at sscu.iisc.ernet.in
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Gromacs-4.0.2: energy minimization error in parallel	version
> 
> Dear all,
> 
> I am trying to use mdrun_mpi for energy minimization over 2/4/8 nodes.
> But in every case the run gets aborted with the following error:
> 
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.0.2
> Source code file: minimize.c, line: 404
> 
> Software inconsistency error:
> state mismatch in do_em_step
> -------------------------------------------------------
> 
> What could be the reason behind this? As far as I remember I have not
> faced this problem in 3.3.3 version. Not that I regularly use parallel
> version for energy minimization, but it would be nice to be able to
> sort out this problem. The PR or MD run goes fine in the same
> settings.
> 
> The mdp file is:
> 
> title           = cg+steep energymin spce watbox
> cpp             = /lib/cpp
> define          = -DFLEXIBLE
> 
> integrator      = cg
> nsteps          = 5000
> nstcgsteep      = 1000
> comm_mode       = linear
> nstcomm         = 1
> 
> emtol           = 1.0
> emstep          = 0.01
> 
> nstxout         = 100
> nstvout         = 100
> nstfout         = 100
> nstlog          = 100
> nstenergy       = 100
> energygrps      = protein sol
> 
> nstlist         = 5
> ns_type         = grid
> pbc             = xyz
> rlist           = 0.9
> 
> coulombtype     = PME
> rcoulomb        = 0.9
> 
> vdwtype         = cut-off
> rvdw            = 1.2
> 
> fourier_spacing = 0.12
> pme_order       = 6
> ewald_rtol      = 1e-6
> optimize_fft    = yes
> 
> constraints     = none
> 
> 
> 
> Thanks,
> Suman.
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